MSExperimentDF
- class pyopenms.dataframes.MSExperimentDF(*args, **kwargs)
Bases:
pyopenms.pyopenms_2.MSExperiment- __init__(*args, **kwargs)
Cython signature: void MSExperiment()
Cython signature: void MSExperiment(MSExperiment &)
Methods
__init__(*args, **kwargs)Cython signature: void MSExperiment()
Cython signature: void addChromatogram(MSChromatogram chromatogram)
Cython signature: void addSpectrum(MSSpectrum spec)
Cython signature: MSChromatogram calculateTIC() Returns the total ion chromatogram
Cython signature: void clear(bool clear_meta_data) Clear all spectra data and meta data (if called with True)
Cython signature: bool clearMetaDataArrays()
Cython signature: void clearMetaInfo() Removes all meta values
Cython signature: void clearRanges() Resets all range dimensions as empty
Cython signature: bool empty()
Cython signature: tuple[np.array[float] rt, np.array[float] mz, np.array[float] inty] get2DPeakDataLong(float min_rt, float max_rt, float min_mz, float max_mz)
Cython signature: MSChromatogram getChromatogram(size_t id_)
Cython signature: libcpp_vector[MSChromatogram] getChromatograms()
Cython signature: String getComment() Returns the free-text comment
Cython signature: libcpp_vector[ContactPerson] getContacts() Returns a reference to the list of contact persons
Cython signature: DateTime getDateTime() Returns the date the experiment was performed
Cython signature: ExperimentalSettings getExperimentalSettings()
Cython signature: String getFractionIdentifier() Returns fraction identifier
Cython signature: HPLC getHPLC() Returns a reference to the description of the HPLC run
Cython signature: String getIdentifier() Retrieve document identifier (e.g.
Cython signature: Instrument getInstrument() Returns a reference to the MS instrument description
Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set
Cython signature: String getLoadedFilePath() Returns the file_name which is the absolute path to the file loaded
Cython signature: int getLoadedFileType() Returns the file_type (e.g.
Cython signature: list[int] getMSLevels()
Cython signature: double getMaxIntensity() Returns the maximum intensity
Cython signature: double getMaxMZ() Returns the maximum m/z
Cython signature: double getMaxRT() Returns the maximum RT
Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or
Cython signature: double getMinIntensity() Returns the minimum intensity
Cython signature: double getMinMZ() Returns the minimum m/z
Cython signature: double getMinRT() Returns the minimum RT
Cython signature: size_t getNrChromatograms() Returns the number of chromatograms
Cython signature: size_t getNrSpectra() Returns the number of MS spectra
Cython signature: int getPrecursorSpectrum(int zero_based_index) Returns the index of the precursor spectrum for spectrum at index @p zero_based_index
Cython signature: void getPrimaryMSRunPath(StringList & toFill) References to the first MS file(s) after conversions.
Cython signature: libcpp_vector[ProteinIdentification] getProteinIdentifications() Returns a reference to the protein ProteinIdentification vector
Cython signature: Sample getSample() Returns a reference to the sample description
Cython signature: uint64_t getSize() Returns the total number of peaks
Cython signature: libcpp_vector[SourceFile] getSourceFiles() Returns a reference to the source data file
Cython signature: libcpp_vector[MSSpectrum] getSpectra()
Cython signature: MSSpectrum getSpectrum(size_t id_)
get_df([long])Generates a pandas DataFrame with all peaks in the MSExperiment
Exports data from MSExperiment to pandas DataFrames to be used with MassQL.
Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty
Cython signature: bool isSorted(bool check_mz)
Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry
Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists
Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists
Cython signature: void reserve(size_t s)
Cython signature: void reserveSpaceChromatograms(size_t s)
Cython signature: void reserveSpaceSpectra(size_t s)
Cython signature: void reset()
Cython signature: void resize(size_t s)
Cython signature: void setChromatograms(libcpp_vector[MSChromatogram] chromatograms)
Cython signature: void setComment(String comment) Sets the free-text comment
Cython signature: void setContacts(libcpp_vector[ContactPerson] contacts) Sets the list of contact persons
Cython signature: void setDateTime(DateTime date_time) Sets the date the experiment was performed
Cython signature: void setFractionIdentifier(String fraction_identifier) Sets the fraction identifier
Cython signature: void setHPLC(HPLC hplc) Sets the description of the HPLC run
Cython signature: void setIdentifier(String id) Sets document identifier (e.g.
Cython signature: void setInstrument(Instrument instrument) Sets the MS instrument description
Cython signature: void setLoadedFilePath(String file_name) Sets the file_name according to absolute path of the file loaded, preferably done whilst loading
Cython signature: void setLoadedFileType(String file_name) Sets the file_type according to the type of the file loaded from, preferably done whilst loading
Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name
Cython signature: void setProteinIdentifications(libcpp_vector[ProteinIdentification] protein_identifications) Sets the protein ProteinIdentification vector
Cython signature: void setSample(Sample sample) Sets the sample description
Cython signature: void setSourceFiles(libcpp_vector[SourceFile] source_files) Sets the source data file
Cython signature: void setSpectra(libcpp_vector[MSSpectrum] & spectra)
Cython signature: int size()
Cython signature: void sortChromatograms(bool sort_rt)
Cython signature: void sortSpectra(bool sort_mz)
Cython signature: void swap(MSExperiment)
Cython signature: void updateRanges()
- addChromatogram()
Cython signature: void addChromatogram(MSChromatogram chromatogram)
- addSpectrum()
Cython signature: void addSpectrum(MSSpectrum spec)
- calculateTIC()
Cython signature: MSChromatogram calculateTIC() Returns the total ion chromatogram
- clear()
Cython signature: void clear(bool clear_meta_data) Clear all spectra data and meta data (if called with True)
- clearMetaDataArrays()
Cython signature: bool clearMetaDataArrays()
- clearMetaInfo()
Cython signature: void clearMetaInfo() Removes all meta values
- clearRanges()
Cython signature: void clearRanges() Resets all range dimensions as empty
- empty()
Cython signature: bool empty()
- get2DPeakDataLong()
Cython signature: tuple[np.array[float] rt, np.array[float] mz, np.array[float] inty] get2DPeakDataLong(float min_rt, float max_rt, float min_mz, float max_mz)
- getChromatograms()
Cython signature: libcpp_vector[MSChromatogram] getChromatograms()
- getComment()
Cython signature: String getComment() Returns the free-text comment
- getContacts()
Cython signature: libcpp_vector[ContactPerson] getContacts() Returns a reference to the list of contact persons
- getDateTime()
Cython signature: DateTime getDateTime() Returns the date the experiment was performed
- getExperimentalSettings()
Cython signature: ExperimentalSettings getExperimentalSettings()
- getFractionIdentifier()
Cython signature: String getFractionIdentifier() Returns fraction identifier
- getHPLC()
Cython signature: HPLC getHPLC() Returns a reference to the description of the HPLC run
- getIdentifier()
Cython signature: String getIdentifier() Retrieve document identifier (e.g. an LSID)
- getInstrument()
Cython signature: Instrument getInstrument() Returns a reference to the MS instrument description
- getKeys()
Cython signature: void getKeys(libcpp_vector[String] & keys) Fills the given vector with a list of all keys for which a value is set
- getLoadedFilePath()
Cython signature: String getLoadedFilePath() Returns the file_name which is the absolute path to the file loaded
- getLoadedFileType()
Cython signature: int getLoadedFileType() Returns the file_type (e.g. featureXML, consensusXML, mzData, mzXML, mzML, …) of the file loaded
- getMSLevels()
Cython signature: list[int] getMSLevels()
- getMaxIntensity()
Cython signature: double getMaxIntensity() Returns the maximum intensity
- getMaxMZ()
Cython signature: double getMaxMZ() Returns the maximum m/z
- getMaxRT()
Cython signature: double getMaxRT() Returns the maximum RT
- getMetaValue()
Cython signature: DataValue getMetaValue(String) Returns the value corresponding to a string, or
- getMinIntensity()
Cython signature: double getMinIntensity() Returns the minimum intensity
- getMinMZ()
Cython signature: double getMinMZ() Returns the minimum m/z
- getMinRT()
Cython signature: double getMinRT() Returns the minimum RT
- getNrChromatograms()
Cython signature: size_t getNrChromatograms() Returns the number of chromatograms
- getNrSpectra()
Cython signature: size_t getNrSpectra() Returns the number of MS spectra
- getPrecursorSpectrum()
Cython signature: int getPrecursorSpectrum(int zero_based_index) Returns the index of the precursor spectrum for spectrum at index @p zero_based_index
- getPrimaryMSRunPath()
Cython signature: void getPrimaryMSRunPath(StringList & toFill) References to the first MS file(s) after conversions. Used to trace results back to original data.
- getProteinIdentifications()
Cython signature: libcpp_vector[ProteinIdentification] getProteinIdentifications() Returns a reference to the protein ProteinIdentification vector
- getSample()
Cython signature: Sample getSample() Returns a reference to the sample description
- getSize()
Cython signature: uint64_t getSize() Returns the total number of peaks
- getSourceFiles()
Cython signature: libcpp_vector[SourceFile] getSourceFiles() Returns a reference to the source data file
- getSpectra()
Cython signature: libcpp_vector[MSSpectrum] getSpectra()
- get_df(long: bool = False)
Generates a pandas DataFrame with all peaks in the MSExperiment
Parameters: long: set to True if you want to have a long/expanded/melted dataframe with one row per peak. Faster but
replicated RT information. If False, returns rows in the style: rt, np.array(mz), np.array(int)
Returns: pandas.DataFrame: feature information stored in a DataFrame
- get_massql_df()
Exports data from MSExperiment to pandas DataFrames to be used with MassQL.
The Python module massql allows queries in mass spectrometry data (MS1 and MS2 data frames) in a SQL like fashion (https://github.com/mwang87/MassQueryLanguage).
Both dataframes contain the columns: ‘i’: intensity of a peak ‘i_norm’: intensity normalized by the maximun intensity in the spectrum ‘i_tic_norm’: intensity normalized by the sum of intensities (TIC) in the spectrum ‘mz’: mass to charge of a peak ‘scan’: number of the spectrum ‘rt’: retention time of the spectrum ‘polarity’: ion mode of the spectrum as integer value (positive: 1, negative: 2)
The MS2 dataframe contains additional columns: ‘precmz’: mass to charge of the precursor ion ‘ms1scan’: number of the corresponding MS1 spectrum ‘charge’: charge of the precursor ion
Returns: ms1_df (pandas.DataFrame): peak data of MS1 spectra ms2_df (pandas.DataFrame): peak data of MS2 spectra with precursor information
- isMetaEmpty()
Cython signature: bool isMetaEmpty() Returns if the MetaInfo is empty
- isSorted()
Cython signature: bool isSorted(bool check_mz) Checks if all spectra are sorted with respect to ascending RT
Cython signature: bool isSorted()
- metaRegistry()
Cython signature: MetaInfoRegistry metaRegistry() Returns a reference to the MetaInfoRegistry
- metaValueExists()
Cython signature: bool metaValueExists(String) Returns whether an entry with the given name exists
- removeMetaValue()
Cython signature: void removeMetaValue(String) Removes the DataValue corresponding to name if it exists
- reserve()
Cython signature: void reserve(size_t s)
- reserveSpaceChromatograms()
Cython signature: void reserveSpaceChromatograms(size_t s)
- reserveSpaceSpectra()
Cython signature: void reserveSpaceSpectra(size_t s)
- reset()
Cython signature: void reset()
- resize()
Cython signature: void resize(size_t s)
- setChromatograms()
Cython signature: void setChromatograms(libcpp_vector[MSChromatogram] chromatograms)
- setComment()
Cython signature: void setComment(String comment) Sets the free-text comment
- setContacts()
Cython signature: void setContacts(libcpp_vector[ContactPerson] contacts) Sets the list of contact persons
- setDateTime()
Cython signature: void setDateTime(DateTime date_time) Sets the date the experiment was performed
- setFractionIdentifier()
Cython signature: void setFractionIdentifier(String fraction_identifier) Sets the fraction identifier
- setHPLC()
Cython signature: void setHPLC(HPLC hplc) Sets the description of the HPLC run
- setIdentifier()
Cython signature: void setIdentifier(String id) Sets document identifier (e.g. an LSID)
- setInstrument()
Cython signature: void setInstrument(Instrument instrument) Sets the MS instrument description
- setLoadedFilePath()
Cython signature: void setLoadedFilePath(String file_name) Sets the file_name according to absolute path of the file loaded, preferably done whilst loading
- setLoadedFileType()
Cython signature: void setLoadedFileType(String file_name) Sets the file_type according to the type of the file loaded from, preferably done whilst loading
- setMetaValue()
Cython signature: void setMetaValue(String, DataValue) Sets the DataValue corresponding to a name
- setProteinIdentifications()
Cython signature: void setProteinIdentifications(libcpp_vector[ProteinIdentification] protein_identifications) Sets the protein ProteinIdentification vector
- setSample()
Cython signature: void setSample(Sample sample) Sets the sample description
- setSourceFiles()
Cython signature: void setSourceFiles(libcpp_vector[SourceFile] source_files) Sets the source data file
- setSpectra()
Cython signature: void setSpectra(libcpp_vector[MSSpectrum] & spectra)
- size()
Cython signature: int size()
- sortChromatograms()
Cython signature: void sortChromatograms(bool sort_rt) Sorts chromatograms by m/z. If sort_rt=True also sort each chromatogram RT
Cython signature: void sortChromatograms()
- sortSpectra()
Cython signature: void sortSpectra(bool sort_mz) Sorts spectra by RT. If sort_mz=True also sort each peak in a spectrum by m/z
Cython signature: void sortSpectra()
- swap()
Cython signature: void swap(MSExperiment)
- updateRanges()
Cython signature: void updateRanges() Recalculate global RT and m/z ranges after changes to the data has been made.
Cython signature: void updateRanges(int msLevel) Recalculate RT and m/z ranges for a specific MS level